biogems.info - gems for bioinformatics

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#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library	BioRuby project	1.5.1	11 months	304	15	150559	0	0
2	biodiversity	Parser of scientific names	Dmitry Mozzherin	3.4.2	2 days	23	3	82140	6	6
3	bio samtools	Binder of samtools for Ruby, on the top	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.5.1	9 months	26	8	59890	0	0
4	bio gem	Biogem is a software generator for Ruby in	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	3 years	15	12	54547	0	0
5	sequenceserver	Blast search made easy!	Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.	1.0.11	8 weeks	114	45	50334	0	0
6	bio gadget		Shintaro Katayama	0.5.0	6 months		1	40594	0	0
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome	Hiroyuki Mishima, Jan Aerts	0.6.3	3 days	16	1	37410	11	11
8	entrez	Http requests to entrez e-utilities	Jared Ning	0.5.8.2	2 years	8	1	34448	0	0
9	bio svgenes	Create pretty svg-format images of features, gene models	Dan MacLean	0.4.1	3 years	14	5	32277	0	0
10	biomart	A Ruby api for interacting with biomart services	Darren Oakley	0.2.3	6 years	17	5	30608	0	0
11	bio maf	Maf parser for BioRuby	Clayton Wheeler	1.0.1	5 years	10	36	27430	0	0
12	bio gff3	Gff3 parser for big data	Pjotr Prins	0.9.1	5 years	7	2	26006	0	0
13	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer	Pjotr Prins	2.0.4	2 years	13	1	25240	0	0
14	bio grid	A biogem to submit jobs on a queue	Francesco Strozzi	0.3.3	4 years	5	...	24279	0	0
15	search biomodel	Interfaces with biomodel search engine	Niall Beard	2.1.6	5 years	1	...	24082	0	0
16	bio polyploid tools	Tool to work with polyploids, ngs and molecular	Ricardo H. Ramirez-Gonzalez	0.7.3	2 years	1	2	23851	0	0
17	biointerchange	An open source framework for transforming heterogeneous data	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	2 years	13	3	21133	0	0
18	bio logger	Log4r wrapper with extra features for roles and	Pjotr Prins	1.0.1	5 years	4	2	21019	0	0
19	obo parser	Ruby parsering for obo files	Matt Yoder	0.4.0	5 years	5	...	20656	0	0
20	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv	Pjotr Prins	1.0.0	3 years	10	21	17709	0	0
21	bio band	Data mining algorithms for jRuby	arrigonialberto86	0.1.11	3 years	16	3	17531	0	0
22	bio alignment	Support for multiple sequence alignments (msa)	Pjotr Prins	0.0.9	10 months	11	5	17227	0	0
23	bio faster	A fast parser for fastq files	Francesco Strozzi	0.4.5	5 years	10	...	16659	0	0
24	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha	George Githinji	0.7.1	4 years			13971	0	0
25	bio vcf	Fast multi-purpose multi-threaded vcf parser	Pjotr Prins	0.9.2	19 months	43	9	13542	0	0
26	bio bigbio	Low memory sequence emitters	Pjotr Prins	0.1.6	3 years	11	1	13519	0	0
27	bio phyta	Pipeline to remove contaminations from est libraries	Philipp Comans	0.9.4	5 years	2	1	13157	0	0
28	bio signalp	A wrapper for the signal peptide prediction algorith	Ben J Woodcroft	0.3.1	3 years	3	...	12995	0	0
29	scaffolder	Build genome output files	Michael Barton	0.5.0	4 years	7	...	12669	0	0
30	nexus parser	A nexus file format (phylogenetic inference) parser in	mjy	1.1.4	6 years	1	...	12610	0	0
31	bio rocker	Rocker	Luis (Coto) Orellana, Luis M. Rodriguez-R	1.1.12	15 months			12554	0	0
32	bio ngs	Bio-ngs provides a framework for handling ngs data	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	5 years	29	15	12536	0	0
33	bio kmer counter	A biogem for counting small kmers for fingerprinting	Ben J Woodcroft	0.1.2	4 years	4	...	12184	0	0
34	bio tm hmm	A BioRuby plugin for interaction with the transmembrane	Ben J. Woodcroft	0.2.4	4 months	2	...	12169	0	0
35	bio basespace sdk	Basespace Ruby sdk is a Ruby based software	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	4 years	11	2	11787	0	0
36	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor	mjy	0.2.6	6 years	1	...	11544	0	0
37	bio sambamba	Ruby wrapper for sambamba tool	Artem Tarasov	0.0.5	5 years	2	...	11336	0	0
38	bio assembly	BioRuby assembly plugin	Chase Miller, Francesco Strozzi	0.1.0	6 years	4	...	11233	0	0
39	eutils	Lightweight Ruby api for ncbi eutils	Joon Lee, aka seouri	0.2.1	4 years	7	1	10995	0	0
40	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point	George Githinji, Pascal Betz	0.1.3	5 years	3	...	10738	0	0
41	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org)	Rutger Vos, Anurag Priyam	1.1.0	5 years	8	2	10656	0	0
42	bio fastqc	Ruby parser for fastqc output	Tazro Inutano Ohta	0.9.1	9 months	2	...	10311	0	0
43	bio velvet	Parser to work with file formats used in	Ben J Woodcroft	0.6.0	2 years		...	10254	0	0
44	bio polymarker db batch	Server for polymarker. to be used with cron	Ricardo H. Ramirez-Gonzalez	0.5.1	2 years		...	10187	0	0
45	bioportal	Supports linking of models within a ror application	Stuart Owen, Quyen Nguyen	2.2	3 years		...	10065	0	0
46	genevalidator	Identifying problems with gene predictions	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.6.12	15 months	1	...	9922	0	0
47	bio bgzf	Reading/writing bgzf blocks	Artem Tarasov, Clayton Wheeler	0.2.1	5 years	3	...	9475	0	0
48	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps	Hiroyuki Mishima	0.1.2	6 years	4	...	9420	0	0
49	bio graphics	Library for visualizing genomic regions	Jan Aerts	1.4	9 years	22	1	9416	0	0
50	taxonifi	A general purpose framework for scripted handling of development/stable	mjy	0.4.0	4 years	2	1	9071	0	0
51	bio octopus	Running and parsing of the protein transmembrane domain	Ben J Woodcroft	0.1.1	6 years	1	...	8618	0	0
52	bio cd hit report	Read and manipulate cd-hit clusters	George Githinji	0.1.0	4 years			8214	0	0
53	bio tabix	Ruby binding for samtools tabix	throwern	1.0.1	3 years	5	1	8043	0	0
54	bio bwa	Ruby binding for bwa mapping software	Francesco Strozzi	0.2.2	6 years	4	...	7968	0	0
55	bio lazyblastxml	A plugin that allows you to parse large	robsyme	0.4.0	6 years	1	...	7703	0	0
56	bio pileup iterator	Iterate through a samtools pileup file	Ben J. Woodcroft	0.0.4	4 years	2	...	7504	0	0
57	bio fasta retrieve	Retrieve dna sequence from ucsc using given coordinates	Andrei Rozanski	0.0.7	2 years			7470	0	0
58	goruby	Gene ontology (go) interface for Ruby	Ben J Woodcroft	0.2.0	6 years	11	...	7426	0	0
59	bio plasmoap	Implementation of the plasmoap algorithm	Ben J Woodcroft	0.1.1	16 months	1	...	7229	0	0
60	ruby ensembl api	Api to ensembl databases	Jan Aerts, Francesco Strozzi	1.0.1	6 years	40	5	6992	0	0
61	bio gff3 pltools	Ruby wrapper for the gff3-pltools	Marjan Povolni	0.3.0	5 years	13	19	6763	0	0
62	bio gngm	Next-generation mapping of mutations	Dan MacLean	0.2.1	4 years	2	...	6702	0	0
63	bio velvet underground	Bindings to some internals of the velvet assembler	Ben Woodcroft	0.3.1	12 months		1	6701	0	0
64	bio statsample timeseries	Timeseries modules for statsample	Ankur Goel, Claudio Bustos	0.2.1	3 years			6675	0	0
65	bio chembl	Chembl rest api client, parser and container	Mitsuteru Nakao	0.1.3	5 years	1	1	6653	0	0
66	publisci	Publish scientific results to the semantic web	Will Strinz	0.1.6	3 years	3	16	6627	0	0
67	bio ucsc util	Ruby binding to the ucsc kent utilities	throwern	0.1.2	4 years	2	...	6576	0	0
68	bio krona	This biogem is built around krona, a flashy	Ben J. Woodcroft	0.2.0	20 months	1	...	6413	0	0
69	bio rdf	Bioinformatics triple-store support	Pjotr Prins	0.0.2	5 years	4	1	6155	0	0
70	bio affy	Parse affymetrix cel/cdf files	Pjotr Prins	0.5.1	5 years	2	1	6138	0	0
71	bio commandeer	Dead simple method of running shell commands from	Ben J. Woodcroft	0.4.0	1 week		...	6117	0	7
72	bio pipengine	A pipeline manager	Francesco Strozzi, Raoul Jean Pierre Bonnal	0.9.6	1 week	15	7	6027	0	26
73	bio kb illumina	Geneexpression illuminahumanannotation	Raoul J.P. Bonnal	0.1.0	6 years	1	...	5917	0	0
74	bio unichem	BioRuby plugin for unichem rest web service	Mitsuteru Nakao	0.3.0	4 years			5801	0	0
75	bio synreport	Reports whether a nucleotide change results in synonymous	Dan MacLean	0.1.2	4 years		...	5709	0	0
76	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)	Andrei Rozanski	1.3.0	3 years	1	...	5524	0	0
77	ref2bibtex	Pass a full citation, get the bibtex back,	Matt Yoder	0.1.1	10 weeks		1	5486	0	12
78	genevalidatorapp	A web app wrapper for genevalidator	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.5.4	11 months	1	...	5398	0	0
79	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser,	Raoul J.P. Bonnal	0.0.1	5 years	1	...	5311	0	0
80	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be	Ben J Woodcroft	0.0.3	5 years	1	...	5134	0	0
81	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal	Ben J. Woodcroft	0.3.0	5 years	2	...	5119	0	0
82	bio protparam	A protparam compatible utility for BioRuby	hryk	0.2.0	4 years	2	1	5096	0	0
83	bio hmmer model	Parse pfam hmm definition files	Ben J. Woodcroft	0.0.2	5 years	1	...	4699	0	0
84	bio gag	Bio-gag is a biogem for detecting and correcting	Ben J Woodcroft	0.1.0	4 years	2	...	4543	0	0
85	bio biostars analytics	Biostars data-mining and statistical analysis	Joachim Baran	0.2.0	3 years			4193	0	0
86	bio locus	Fast storage and comparison of chr+pos(+alt) locations	Pjotr Prins	0.0.7	23 months	2	1	3970	0	0
87	nbio cloudquery	Client for xoopit's cloudquery api	Cameron Walters, nb.io	0.1.5	8 years	5	...	3953	0	0
88	bio hmmer3 report	Enables parsing of hmmer version 3 reports	Christian Zmasek, Ben J Woodcroft	0.1.0	2 years	2	1	3784	0	0
89	ncbi blast dbs	Fast download blast databases from ncbi beta	Anurag Priyam	0.0.6	3 months	5	2	3774	0	0
90	bio sra	A sequence read archive (sra) download script and	Ben J. Woodcroft	0.3.1	20 months	3	...	3701	0	0
91	bio gggenome	Gggenome Ruby client	Mitsuteru Nakao	0.2.0	4 years	1	...	3611	0	0
92	bio ensembl rest	Ruby ensembl rest api	Alberto Donizetti	0.2.0	3 years	2	...	3567	0	0
93	rubyBHL	Rubybhl is a simple request/response wrapper for the	Matt Yoder	0.2.1	3 years	6	...	3484	0	0
94	bio statsample glm	Generalized linear models for statsample	Ankur Goel	0.1.1	3 years			3427	0	0
95	bio express beta diversity	Interface for express beta diversity	Ben J. Woodcroft	0.1.0	3 years		...	3232	0	0
96	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a	Cameron Walters, Randy Reddig	1.0.3	8 years	90	1	3160	0	0
97	bio sge	BioRuby plugin for sun grid engine	Toshiaki Katayama	0.0.0	6 years	4	...	3158	0	0
98	bio repeatmasker	Bio-repeatmasker	Andrei Rozanski	0.0.3	3 years		...	3155	0	0
99	bio hello	Hello world plugin for the BioRuby (just for	Toshiaki Katayama	0.0.0	6 years	3	...	3144	0	0
100	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns	Trevor Wennblom	1.0.0	5 years		1	3091	0	0
101	bio mummer	Helper methods for reading .delta files	robsyme	0.2.1	2 years		...	3076	0	0
102	bio cigar	A parser for cigar format alignments	Ben J Woodcroft	0.1.0	3 years	4	...	3025	0	0
103	dna sequence aligner	Does high pairwise alignment of sequencing reads with	John T. Prince	0.0.2	7 years	1	...	3025	0	0
104	bio ipcress	A programmatic interface to the ipcress in-silico pcr	Ben J Woodcroft	0.1.0	7 months	3	...	2982	0	0
105	bio samtools server	Web server for bio-samtools	homonecloco	0.1.2	3 years		...	2933	0	0
106	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of	Ben J Woodcroft	0.1.0	6 years	1	...	2915	0	0
107	bio core ext	BioRuby core ext: plugins which require external library	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	5 years	1	...	2857	0	0
108	bio biolinux	Meta package for biolinux distribution	Raoul J.P. Bonnal	0.1.0	5 years	2	...	2851	0	0
109	bio ensembl	A Ruby api to the ensembl database	Jan Aerts, Francesco Strozzi	1.1.0	5 years	4	...	2825	0	0
110	bio foo	One-line summary of your gem	Toshiaki Katayama	0.0.0	5 years	1	...	2810	0	0
111	bio data restriction enzyme	Restriction enzyme dataset	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	5 years		...	2809	0	0
112	bio dbsnp	Decoding the dbsnp bitfield	Hiroyuki Mishima	0.1.1	5 years	4	...	2773	0	0
113	intermine bio	Biological extensions for the intermine webservice client library	Alex Kalderimis	0.98.1	6 years	1	...	2765	0	0
114	bio hydropathy	Hydropathy scale for BioRuby	Ben J Woodcroft	0.0.1	5 years	1	...	2758	0	0
115	bio exportpred	Wrapper around the exportpred algorithm for predicting p	Ben J Woodcroft	0.0.1	5 years	1	...	2749	0	0
116	bio phyloxml	Phyloxml plugin for BioRuby	Diana Jaunzeikare, Clayton Wheeler	0.9.0	5 years	3	1	2747	0	0
117	bio aliphatic index	A simple biogem that allows computation of the	Ben J Woodcroft	0.0.1	5 years	1	...	2724	0	0
118	bio incanter	Build graph with jRuby	Matteo Picciolini	0.1.0	5 years			2553	0	0
119	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives	Naohisa Goto	1.0.0	14 months		...	2317	0	0
120	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata	Ben J. Woodcroft	0.0.1	4 years		...	2301	0	0
121	bio stockholm	Parse stockholm sequence alignment format	Ben J. Woodcroft	0.0.1	4 years	2	...	2123	0	0
122	bio gfastqc	Aggregate fastqc (quality control for next generation sequencing	Raoul Jean Pierre Bonnal	0.0.4	2 years		...	2081	0	0
123	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood	Fernando Izquierdo	0.1.0	4 years		...	2035	0	0
124	bio freebayes	The api for freebayes version #{bio::freebayes::extversion}	Natapol Pornputtapong	0.1.6	2 years			2014	0	0
125	bio kseq	Ruby inferface for kseq.h by heng li for	Fedor Gusev	0.0.2	3 years	1	...	1826	0	0
126	bio exominer	Mine publications for gene names	Pjotr Prins	0.0.3	3 years	1	...	1658	0	0
127	bark	A Ruby wrapper on the open tree api beta	Matt Yoder	0.0.2	2 years	1	...	1563	0	1
128	genomichdt	A restful service for sharing genomic data	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	3 years			1531	0	0
129	bio faidx	Tools to work with fasta files, indexed with	homonecloco	0.0.1	2 years		...	1490	0	0
130	bio blat tools	Tools to manipulate blat files from the command	homonecloco	0.1.0	2 years		...	1464	0	0
131	bio location rdfize	Faldo location output method for bio::location in BioRuby	Joachim Baran, Naohisa Goto	0.0.0	2 years		...	1428	0	0
132	bio picard	Api of picard tool	Natapol Pornputtapong	1.131.5	2 years			1337	0	0
133	nbio css http request	Csshttprequest is cross-domain ajax using css disabled	Cameron Walters, Randy Reddig	0.1	8 years			1286	0	0
134	bio sparql client	A Ruby wrapper for bio sparql service	Natapol Pornputtapong	0.0.1	2 years			1282	0	0
135	bio conduit	A pipeline creator for BioRuby	Natapol Pornputtapong	1.0.0	23 months			1055	0	0
136	bio jaspar	Tools for jaspar motifs in BioRuby	Jessica Lee, Wasserman Lab	0.1.0	23 months		...	1054	0	0
137	bio kallisto	Basic wrapper for the kallistio mapper	homonecloco	0.1.0	22 months	1	...	1028	0	0
138	bio plates	Methods for handling multiwell plate annotations	Steve Pettitt	0.2.0	18 months		...	869	0	0
139	bio sam mutation	Parsing and mutation calling from sam, cigar and	Stephen Pettitt	0.4.1	18 months		...	817	0	0
140	bio biosql	Biosql plugin for BioRuby	BioRuby project	0.0.0	14 months		...	576	0	0
141	bio primer3	pre		pre			...	0	0	0

*) gem downloads (total & last 90 days) from rubygems.org as of 2017-08-20
**) number of commits on GitHub (last 7 days & last 90 days)